Merge pull request #88 from nlmixr2/87-tad-calculation-inconsistent

Fix zero dose + evid=2 to not be counted as dose
nlmixr2 · Feb 7, 2024 · cfeb768 · cfeb768
2 parents 8249e25 + c3d8fcf
commit cfeb768
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Showing 5 changed files with 20 additions and 9 deletions.
diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,6 +1,6 @@
 Package: rxode2parse
 Title: Parsing and Code Generation Functions for 'rxode2'
-Version: 2.0.18
+Version: 2.0.18.9000
 Authors@R: c(
     person("Matthew L.", "Fidler", , "matthew.fidler@gmail.com", role = c("aut", "cre"),
            comment = c(ORCID = "0000-0001-8538-6691")),

diff --git a/NEWS.md b/NEWS.md
@@ -1,3 +1,7 @@
+# rxode2parse (development version)
+
+* Added a evid suffix of 60 for cases where evid=2 adds an on event
+
 # rxode2parse 2.0.18
 
 * Removed linear compartment solutions with gradients from rxode2parse

diff --git a/inst/include/rxode2parseHandleEvid.h b/inst/include/rxode2parseHandleEvid.h
@@ -99,6 +99,7 @@ extern "C" {
 // xx = 30, Turn off compartment
 // xx = 40, Steady state constant infusion
 // xx = 50, Phantom event, used for transit compartments
+// xx = 60, Dose that does not track as a dose turn on system
 // Steady state events need a II data item > 0
 #define EVID0_REGULAR  1
 #define EVID0_RATEADJ 2
@@ -110,7 +111,7 @@ extern "C" {
 #define EVID0_OFF 30
 #define EVID0_SSINF 40
 #define EVID0_PHANTOM 50
-
+#define EVID0_ONDOSE 60
 
 static inline void getWh(int evid, int *wh, int *cmt, int *wh100, int *whI, int *wh0){
   *wh = evid;
@@ -229,6 +230,12 @@ static inline int handleTlastInlineUpateDosingInformation(rx_solving_options_ind
     }
     break;
   }
+  if (ind->wh0 == EVID0_ONDOSE) {
+    // evid=2 can add zero dose to turn on a compartment;
+    // therefore if the current dose is zero and the next evid = 2
+    // don't treat it as a new dose.
+    return 0;
+  }
   return 1;
 }
 

diff --git a/src/etTran.cpp b/src/etTran.cpp
@@ -1220,7 +1220,7 @@ List etTransParse(List inData, List mv, bool addCmt=false,
     else caddl = inAddl[i];
     if (IntegerVector::is_na(caddl)) caddl = 0;
     // EVID flag
-    if (evidCol == -1){
+    if (evidCol == -1) {
       // Missing EVID
       if (rateI == 0 && (ISNA(camt) || camt == 0.0)){
         cevid = 0;
@@ -1252,7 +1252,7 @@ List etTransParse(List inData, List mv, bool addCmt=false,
         cevid=0;
       }
     }
-    switch(cevid){
+    switch(cevid) {
     case 0:
       // Observation
       nobs++;
@@ -1417,10 +1417,10 @@ List etTransParse(List inData, List mv, bool addCmt=false,
         ndose++;
         // + cmt needs to turn on cmts.
         // This gives a zero dose to cmt
-        if (cmtCol != -1 && cmt > 0 && cmt <= baseSize){
+        if (cmtCol != -1 && cmt > 0 && cmt <= baseSize) {
           // Turn on state with dose
           id.push_back(cid);
-          evid.push_back(cevid);
+          evid.push_back(cevid-flg+60);
           cmtF.push_back(cmt);
           time.push_back(ctime);
           amt.push_back(0.0);

diff --git a/tests/testthat/test-etTrans.R b/tests/testthat/test-etTrans.R
@@ -18,7 +18,7 @@ d/dt(blood)     = a*intestine - b*blood
                   class = "data.frame",
                   row.names = c(NA,-6L))
   skip_on_cran()
-  
+
   expect_warning(expect_false(any(is.na(etTransParse(et, mod)$TIME))))
 })
 
@@ -139,7 +139,7 @@ d/dt(blood)     = a*intestine - b*blood
                        evid = c(1L, 2L, 2L)),
                   class = "data.frame",
                   row.names = c(NA, -3L))
-  
+
   test_that("error for negative non ODE compartments", {
     expect_error(etTransParse(et, mod, keepDosingOnly = TRUE))
     et$cmt <- factor(et$cmt)
@@ -534,7 +534,7 @@ d/dt(blood)     = a*intestine - b*blood
   })
 
   test_that("dat3 has evid w/amt 0", {
-    expect_equal(dat3$EVID, c(101L, 2L, 0L, 0L, 0L, 101L, 2L, 0L, 0L, 0L))
+    expect_equal(dat3$EVID, c(160L, 2L, 0L, 0L, 0L, 160L, 2L, 0L, 0L, 0L))
     expect_equal(dat3$AMT, c(0, NA, NA, NA, NA, 0, NA, NA, NA, NA))
   })